Only bad ones are Scarecrow's and Bane's in my opinion, but it's not like they were very good or compelling villains anyway. Scarecrow's was pretty disappointing, because it felt like we finally got a fully realized, intimidating Scarecrow so a tazer to the face screaming is a buzz kill. I think everyone expected a final confrontation with Batman before he headed off to face Ra's. But whatever.
Bane? Don't even care. He was a pretty poor character in general, especially after how great the Joker was, not like it matters if he had a cool ending/death/defeat. Same goes for Talia. At least she had a laughably bad death scene. It sure wasn't boring to come back from the show and see all the criticism regarding her death scene.
I think Joker's was fine, it's just a shame we never got to see more of him again. What did people want? It was either going to end with him being captured or hav him die. We get a great scene of him finally being subdued, upside down and having a great speech to Batman. The last shot is the SWAT team moving in and he does that fantastic, hysterical laugh where it looks like he's crying and in tears.
This might have been cool to include in TDK's montage. Maybe have him getting thrown into the car and having it drive away, and he overhears cops over the police radio that they're pursuing a new suspect, the Batman. Cut away and show a final smile on his face.
I'd like to think they shot that after the Prewitt siege, but it was most likely after he's apprehended by Gordon after the street scene while Dent is talking to the media/press. Too bad it was never included. Would have made nice symmetry with the scene where he's hanging out of the car window.
Two-Face? While I wish they delved into the split personality and rich characterization from the comics, the final ending would have been different had he lived. We were never going to get "Two-Face" as most people know him, so the end is fitting for what it is. I like the contrast between "White Knight" and "Dark Knight" and having the two of them laying at the bottom of the hole. Two-Face literally falls, but Batman takes the fall. Batman also breaks his one rule to save an innocent child. It's appropriate.
Ra's? While I don't agree with the fact that Batman just lets him die (just as bad as killing really) with a sadistic quip, I do like how he man's up and calmly meditates and accepts his fate. I don't think he had a poor ending.
But Scarecrow and Bane? Yeah, I agree.